of Subsequent Local Immune Challenge
Friedrich Felix Hoyer, Kamila Naxerova, Maximilian J. Schloss, Maarten Hulsmans, Anil V.
Nair, Partha Dutta, David M. Calcagno, Fanny Herisson, Atsushi Anzai, Yuan Sun, Gregory Wojtkiewicz, David Rohde, Vanessa Frodermann, Katrien Vandoorne, Gabriel Courties, Yoshiko Iwamoto, Christopher S. Garris, David L. Williams, Sylvie Breton, Dennis Brown, Michael Whalen, Peter Libby, Mikael J. Pittet, Kevin R.
King, Ralph Weissleder, Filip K. Swirski, and Matthias Nahrendorf
70%
SSC-A MHCII - Alexa 700
SSC-A
FSC-A
CD64 - Alexa 647 SiglecF - BV421
CD11b - APC-Cy7
CD11c - BV510
SSC-A MHCII - Alexa 700
SSC-A
FSC-A
CD64 - Alexa 647 SiglecF - BV421
CD11b - APC-Cy7
CD11c - BV510
SSC-A MHCII - Alexa 700
SSC-A
FSC-A
CD64 - Alexa 647 SiglecF - BV421
CD11b - APC-Cy7
CD11c - BV510
SSC-A MHCII - Alexa 700
SSC-A
FSC-A
CD64 - Alexa 647 SiglecF - BV421
CD11b - APC-Cy7 gated on viable, single cells
CD11b - APC-Cy7
Lin + Ly6g - PE
FSC-A
CD64 - Alexa 647
Ly6c - FITC
CD64 - Alexa 647
Ly6c - FITC
CD64 - Alexa 647
Ly6c - FITC
F4/80 - PE-Cy7
Stroke gated on viable, single cells
Lin + Ly6g - PE CD64 - Alexa 647 F4/80 - PE-Cy7
CD11b - APC-Cy7
CD45 - BV711
Ly6c - FITC FSC-A CD11b - APC-Cy7
67% 95% 98% 98%
Control
Lin + Ly6g - PE CD64 - Alexa 647 F4/80 - PE-Cy7
CD11b - APC-Cy7
CD45 - BV711
Ly6c - FITC FSC-A CD11b - APC-Cy7
62% 93% 99% 98%
Lin + Ly6g - PE CD64 - Alexa 647 F4/80 - PE-Cy7
CD11b - APC-Cy7
CD45 - BV711
Ly6c - FITC FSC-A CD11b - APC-Cy7
76% 84% 98% 99%
gated on viable, single cells
MI
CD64 - Alexa 647
12%
CD64 - Alexa 647
15%
CD64 - Alexa 647
CD11b - APC-Cy7
F4/80 - PE-Cy7
CD45 - PerCP-Cy5
Lin + Ly6g - PE
SSC-A
CD64 - Alexa 647
gated on viable, single cells
MI
CLP
CD45 - PerCP-Cy5
Lin + Ly6g - PE
SSC-A
CD64 - Alexa 647
CD11b - APC-Cy7
CD64 - Alexa 647
CD11b - APC-Cy7
CD64 - Alexa 647
CD11b - APC-Cy7
CD64 - Alexa 647
CD11b - APC-Cy7
F4/80 - PE-Cy7
14%
86% 89%
Figure S1
gated on viable, single cells
A B
C
D
E
Figure S1. Flow cytometry gating strategy for all organs and conditions, Related to Figure 1-4.
Gating for macrophages in (A) lung, (B) heart, (C) brain, (D) kidney and (E) liver followed the
Immgen guidelines whenever available. By design, the gates include both, resident and newly
recruited macrophages.
MI Con 15
7
*
Recruited renal macrophages (%) Monocytes (102)/ mg liver
28
Neutrophils (102) mg liver
** Recruited renal macrophages (%)
* Interstitial macrophages (102)/ mg lung
14
gated on CD11clow MHCIIhigh B
Figure S2 Cx3cr1-YFPCreER/+
R26-tdTomatotdTomato/+
100 50
tdTomatohigh Ly6c monocytes (%)
day 1 21
Digested lung BAL BAL d4 after MI Interstitial macrophages % of CD64+ cells
F C
Cx3cr1CreER/+ R26tdTomato/+wildtype 6% 63% 93% 0%25%
15% 45% 12% 93% 0.1%
12% 44% 15% 87% 0.03%
Cx3cr1CreER/+ R26tdTomato/+ CD11c
SSC-A MHCII
YFPhigh alveolar macrophages (%)
Con
gated on alveolar macrophages
0.06%
BrdU+ alveolar macrophages (%)
**
BrdU+ alveolar macrophages (%) Con MI
flow BrdU pulse for 14d via drinking waterMI d1d14d15d19
G
Monocytes (103)/ mg lung 1.5
3 ****
**
MI
Neutrophils (103)/ mg lung 1.5
Monocytes (103)/ mg lung 0.7 1.4
Neutrophils (103)/ mg lung 1.5
Neutrophils (103) mg lung
days
Monocytes (101)/ mg heart Stroke Neutrophils (102)/ mg heart
Con 1 4 Monocytes (102)/ mg heart
CLP
***
Con 1 4 71428 63 8
4 Neutrophils (102)/ mg heart
CLP
Monocytes (102)/ mg liver 5 2.5 Neutrophils (102) mg liver
MI
************
Con 1 4 7 1421 Monocytes (102)/ mg liver 1
0.5
***
5 2.5 Neutrophils (102) mg liver **
Con 1 4 7 Stroke
Stroke
Con 1471428 day
CD11bhigh macro phages (103)/ mg liver
1.5
YFPhigh recruited liver macrophages (%)
O
**
Recruited CD45.1 macrophages (%) 10
YFPhigh tdTomatolow macrophages (%)
***
Gated on liver macrophages ****
Q
R
S
T
Renal macro- phages in SG2M % Con
Monocytes (101)/ mg kidney
CLP
**** *
15 7.5
Neutrophils (101)/ mg kidney
Con 134 714 2863
**** ****
CLP
7 ********
3.5 Monocytes (101)/ mg kidney
MI
******
**
8
4 Neutrophils (101)/ mg kidney
Stroke 4 2 Monocytes (101)/ mg kidney
Stroke Neutrophils (101)/ mg kidney
Con 1 4 7 day
YFPYFPhigh tdTomatolow renal macrophages (%)30
15
Renal macrophages in SG2M %
Con 134 7 1428 63
CD31 F4/80
Control CLP d4
Neutrophils (101)/ mg brain
X
MI 1.2
2.4
Monocytes (101)/ mg brain ****
Neutrophils (101)/ mg brain 2 CD45high macrophages (101)/ mg brain
W 6
CD45high macrophages (101)/ mg brain
Figure S2. Myeloid cells and macrophage fate mapping after remote injury in the lung, heart, liver and kidney, Related to Figure 1.
(A) Interstitial macrophages after injury. Control n=19-28, MI n=4-12, stroke n=8-13, CLP n=5-10 biological replicates. (B) Fate mapping in Cx3cr1
CreER/+R26
tdTomato/+mice and quantification of fluorescent proteins in blood monocytes, day 1 n=9, day 21 n=9. (C) Fate mapping for alveolar macrophages in Cx3cr1
CreER/+R26
tdTomato/+mice after MI and CLP and naive Cx3cr1
CreER/+
R26
tdTomato/+controls. Control n=8, MI n=10, CLP n=6 biological replicates. (D) Fate mapping experiments for alveolar macrophages in CD45.1/2 parabionts. MI was induced in DC45.2 mouse, whose lung was then investigated. MI n=2 pairs, naive control n=2 pairs. (E)
Proliferation of alveolar macrophages by BrdU flow cytometry. Left: BrdU was injected i.p. three hours before sacrifice, n=8-10. Right: BrdU pulse chase experiment, n=6-8. (F) FACS of
bronchoalveolar lavage (BAL) in naive controls and day 4 after MI. Naive controls (digested) n=4, controls BAL n=5, MI n=5 biological replicates. (G) Lung monocytes and neutrophils after MI, n=4-30; after stroke, n=8-19; and after CLP, n=5-21 biological replicates. (H) Fate mapping for cardiac macrophages in Cx3cr1
CreER/+R26
tdTomato/+mice after CLP and naive Cx3cr1
CreER/+
R26
tdTomato/+controls. Control n=8, CLP n=12 biological replicates. (I) Fate mapping for cardiac macrophages in CD45.1/2 parabionts after CLP. MI n=6 pairs, naive control n=6 pairs. (J) Cardiac monocytes and neutrophils after stroke, n=4-18 biological replicates per time point; and after CLP, n=5-20. (K) Cell cycle analysis of cardiac macrophages after CLP, naive control n=5, CLP n=4 biological replicates. (L) Fluorescence images of hepatic macrophages at baseline and 4 days after CLP. Scale bar, 50 µm. (M) Hepatic monocytes and neutrophils after MI, n=4-31;
after stroke, n=5-19; and after CLP, n=5-16. (N) Hepatic CD11b
highmacrophages, control n=16-32, MI n=4-12, stroke n=5-13, CLP n=5-6 biological replicates. (O) Fate mapping for hepatic macrophages in Cx3cr1
CreER/+R26
tdTomato/+mice after CLP or MI and naive Cx3cr1
CreER/+
R26
tdTomato/+controls. Control n=7, MI n=9, CLP n=9 biological replicates. (P) Histology of renal macrophages after CLP, Scale bar, 50 µm. (Q) Proliferation of renal macrophages by Ki-67 and Propidium iodide (PI) flow cytometry on d7 after MI, n=7-12. (R) Recruitment of renal
macrophages after MI assessed by parabiosis, n=5-8. (S) Cell cycle analysis in renal
macrophage on d7 after CLP, n=4-6 biological replicates. (T) Recruitment of renal macrophages after CLP assessed by parabiosis, n=10-11; and (U) after MI and CLP in Cx3cr1
CreER/+
R26
tdTomato/+mice, n=3-6. (V) Renal monocytes and neutrophils after MI, n=4-34; after stroke, n=4-16; and after CLP, n=5-29. (W) Brain CD45
highmacrophages after MI and CLP, n=8-14 biological replicates per time point. (X) Monocytes and neutrophils in the brain after MI, n=8 and after CLP, n=8-14. (Y) Fate mapping for microglia in Cx3cr1
CreER/+R26
tdTomato/+mice after CLP, after MI and in and naive Cx3cr1
CreER/+R26
tdTomato/+controls. Control n=5, MI n=8, CLP n=6 biological replicates. Data are mean ± s.e.m. *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001.
One-way ANOVA with Dunnett’s multiple comparison test was applied for normally distributed
data.
A
Figure S3
Enrichment plot: Goldrath antigen response
Brain Lung
Enrichment plot: Goldrath antigen response
Brain Heart
Enrichment plot: Goldrath antigen response
Brain Kidney
Enrichment plot: Goldrath antigen response
Brain Liver
Enrichment plot: Galindo immune response to enterotoxin
Brain Lung
Enrichment plot: Galindo immune response to enterotoxin
Brain Heart
Enrichment plot: Galindo immune response to enterotoxin
Brain Kidney
Enrichment plot: Galindo immune response to enterotoxin
Brain Liver
Brain.Control Brain.MI Brain.Sepsis Heart.Control Heart.Sepsis Heart.Stroke Kidney.Control Kidney.MI Kidney.Sepsis Kidney.Stroke Liver.Control Liver.MI Liver.Sepsis Liver.Stroke Lung.Control Lung.MI Lung.Sepsis Lung.Stroke
Condition
Brain.Control Brain.MI Brain.Sepsis Heart.Control Heart.Sepsis Heart.Stroke Kidney.Control Kidney.MI Kidney.Sepsis Kidney.Stroke Liver.Control Liver.MI Liver.Sepsis Liver.Stroke Lung.Control Lung.MI Lung.Sepsis Lung.Stroke
Condition
Brain.Control Brain.MI Brain.Sepsis Heart.Control Heart.Sepsis Heart.Stroke Kidney.Control Kidney.MI Kidney.Sepsis Kidney.Stroke Liver.Control Liver.MI Liver.Sepsis Liver.Stroke Lung.Control Lung.MI Lung.Sepsis Lung.Stroke
Condition
Brain.Control Brain.MI Brain.Sepsis Heart.Control Heart.Sepsis Heart.Stroke Kidney.Control Kidney.MI Kidney.Sepsis Kidney.Stroke Liver.Control Liver.MI Liver.Sepsis Liver.Stroke Lung.Control Lung.MI Lung.Sepsis Lung.Stroke
Condition
Brain control Brain MI Brain CLP Heart CLP Heart stroke Kidney control Kidney MI Kidney CLP Kidney stroke Livercontrol Liver MI Liver CLP Liver stroke Lung control Lung MI Lung CLP Lung stroke
Brain control Brain MI Brain CLP Heart control Heart CLP Heart stroke Kidney control Kidney MI Kidney CLP Kidney stroke Liver control Liver MI Liver CLP Liver stroke Lung control Lung MI Lung CLP Lung stroke
NES -2.45
Brain control Brain MI Brain CLP Heart CLP Heart stroke Kidney control Kidney MI Kidney CLP Kidney stroke Livercontrol Liver MI Liver CLP Liver stroke Lung control Lung MI Lung CLP Lung stroke
Heart control
Figure S3. Organ specific macrophage expression changes after injury, Related to Figure 2 and 3.
(A) Gene set enrichment analysis of the gene set “GOLDRATH_ANTIGEN_RESPONSE“ in brain microglia vs. all other organs. FDRs are calculated by gene set permutation. (B) Gene set enrichment analysis of the gene set “GALINDO_IMMUNE_RESPONSE_TO_ENTEROTOXIN“
in brain microglia vs. all other organs. (C) Expression (RMA log2 signal) of Cxcl2, (D) Ccl12, (E)
Tnfsf9 across the entire data set.
Interstitial macrophages (102)/ mg lung
2.5 Interstitial macrophages (102)/ mg lung
2.5 5
G
gated on CD11chigh, MHCIIhigh
Alveolar
Egfr expression fold-change over control
1
LysM Egfr+/+Sham n=10 LysM Egfr-/- Sham n=12
Control CloLip MI MI + CloLip
K
LysM Egfr-/- Sham thoracotomy + Pneumonia LysM Egfr+/+ Sham thoracotomy + Pneumonia Naive LysM Egfr+/+
4
Figure S4. Alveolar macrophages after MI, Related to Figure 5.
(A) Bioluminescence signal 2 days after instillation of bioluminescent bacteria in naive controls, on day 6 after MI and day 6 after sham thoracotomy surgery. Control n=39, MI n=23, sham thoracotomy n=18. (B) Flow plots of lung interstitial macrophages in wildtype and Ccr2
-/-mice after MI. (C) Quantification of lung interstitial macrophages in wildtype and Ccr2
-/-mice after MI, n=4-5. (D) Ccr2
-/-mice were subjected to MI and received bioluminescent streptococcus 4 days later, n=8-15. (E) Alveolar macrophages were depleted via intra-tracheal instillation of
clodronate liposome. Flow plots shows macrophages in naive control and after liposome treatment. (F) Quantification of alveolar macrophages over time after clodronate depletion, n=2-4 biological replicates per time point. (G) Flow cytometry for interstitial lung macrophages after intratracheal clodronate liposome instillation. Con n=4, Clolip n=4 biological replicates. (H) Bioluminescence signal 2 days after instillation of bioluminescent bacteria in naive controls, controls that received intratracheal clodronate liposomes, and on day 6 after MI with and without intratracheal clodronate. Naive control n=27, control with clodronate n=12, MI n=11, MI with clodronate n=12. (I) Expression of Egfr in flow sorted alveolar macrophages, interstitial lung macrophages and plasmacytoid dendritic cells. Naive control n=5-6 biological replicates, MI n=6, Pneumonia n=6. (J) Survival analysis in mice with sham thoracotomy. Sham LysM Egfr
-/-n=12, LysM Egfr
+/+n=12. (K) Gene expression in lung tissue harvested from mice that
underwent sham thoracotomy control procedures and induction of pneumonia. Naive LysM Egfr
+/+n=x, Sham LysM Egfr
-/-n=8, LysM Egfr
+/+n=7. Data are mean ± s.e.m. *P<0.05,
**P<0.01, ***P<0.001, ****P<0.0001. Unpaired t-test or ordinary one-way ANOVA with Dunnett’s
multiple comparison test was used for analysis.
Figure S5. Gene expression changes in lung and heart macrophages, Related to Figure 5.
(A) Experimental outline. (B) Gene expression in alveolar macrophages, (C) interstitial lung macrophages, (D) plasmacytoid dendritic cells, (E) neutrophils in naive LysM Egfr
+/+n=2-4, LysM Egfr
+/+with MI and pneumonia n=4-8, LysM Egfr
-/-with MI and pneumonia n=4-8 biological replicates. (F) Gene expression in alveolar macrophages after sham thoracotomy control
procedure and pneumonia. LysM Egfr
+/+naive n=4, LysM Egfr
+/+Sham thoracotomy +
Pneumonia n=4-8, LysM Egfr
-/-Sham thoracotomy + Pneumonia n=4-8 biological replicates.
(G) Bioluminescence imaging after 10µg of intratracheal IFNɣ and intratracheal streptococcus pneumoniae instillation. Data are mean ± s.e.m. *P<0.05. Unpaired t-test or ordinary one-way ANOVA with Dunnett’s multiple comparison test was used for analysis.
12
LysM Egfr-/- Sham thoracotomy + Pneumonia LysM Egfr+/+ Sham thoracotomy + Pneumonia LysM Egfr+/+ naive
4 0 days
Sham Lung infection FACS Pneumonia
Cd11cCre/+ Ifngr1flox/flox
KLRB1C NK cells
YFP-IFNg
modal
KLRB1C NK cells KLRB1C NK cells
Flow
NK cells (102)/ mg cardiac tissue 3 6 ****
Con MI
Con MI NK cells (103)/ ml
2
CD8 T cells CD24 CD103 CD8 T cells CD24 CD103 DCs
DCs
CD8 T cells CD4 T cells CD11b Myeloid cells
YFP-IFNg
modal